[English] 日本語
Yorodumi
- PDB-1lqj: ESCHERICHIA COLI URACIL-DNA GLYCOSYLASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1lqj
TitleESCHERICHIA COLI URACIL-DNA GLYCOSYLASE
ComponentsURACIL-DNA GLYCOSYLASE
KeywordsHYDROLASE / GLYCOSYLASE / DNA REPAIR / BASE EXCISION
Function / homology
Function and homology information


base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / uracil DNA N-glycosylase activity / cytoplasm
Similarity search - Function
Uracil-DNA glycosylase family 1 / Uracil DNA glycosylase superfamily / UreE urease accessory protein, C-terminal domain / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily ...Uracil-DNA glycosylase family 1 / Uracil DNA glycosylase superfamily / UreE urease accessory protein, C-terminal domain / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uracil-DNA glycosylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsSaikrishnan, K. / Sagar, M.B. / Ravishankar, R. / Roy, S. / Purnapatre, K. / Varshney, U. / Vijayan, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Domain closure and action of uracil DNA glycosylase (UDG): structures of new crystal forms containing the Escherichia coli enzyme and a comparative study of the known structures involving UDG.
Authors: Saikrishnan, K. / Bidya Sagar, M. / Ravishankar, R. / Roy, S. / Purnapatre, K. / Handa, P. / Varshney, U. / Vijayan, M.
#1: Journal: Nucleic Acids Res. / Year: 1998
Title: X-ray analysis of a complex of Escherichia coli uracil DNA glycosylase (ECUDG) with a proteinaceous inhibitor. The structure elucidation of a prokaryotic UDG
Authors: Ravishankar, R. / Sagar, M.B. / Roy, S. / Purnapatre, K. / Handa, P. / Varshney, U. / Vijayan, M.
#2: Journal: Protein Expr.Purif. / Year: 1998
Title: Use of a coupled transcriptional system for consistent overexpression and purification of UDG-UGI complex and ugi from Escherichia coli
Authors: Roy, S. / Purnapatre, K. / Handa, P. / Boyanapalli, M. / Varshney, U.
#3: Journal: J.Mol.Biol. / Year: 1999
Title: Protein mimicry of DNA from crystal structures of the uracil-DNA glycosylase inhibitor protein and its complex with Escherichia coli uracil-DNA glycosylase.
Authors: Putnam, C.D. / Shroyer, M.J.N. / Lundquist, A.J. / Mol, C.D. / Arvai, A.S. / Mosbaugh, D.W. / Tainer, J.A.
History
DepositionMay 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: URACIL-DNA GLYCOSYLASE
B: URACIL-DNA GLYCOSYLASE
C: URACIL-DNA GLYCOSYLASE
D: URACIL-DNA GLYCOSYLASE


Theoretical massNumber of molelcules
Total (without water)102,9014
Polymers102,9014
Non-polymers00
Water3,153175
1
A: URACIL-DNA GLYCOSYLASE


Theoretical massNumber of molelcules
Total (without water)25,7251
Polymers25,7251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: URACIL-DNA GLYCOSYLASE


Theoretical massNumber of molelcules
Total (without water)25,7251
Polymers25,7251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: URACIL-DNA GLYCOSYLASE


Theoretical massNumber of molelcules
Total (without water)25,7251
Polymers25,7251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: URACIL-DNA GLYCOSYLASE


Theoretical massNumber of molelcules
Total (without water)25,7251
Polymers25,7251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.210, 125.210, 90.047
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Cell settingtrigonal
Space group name H-MP32

-
Components

#1: Protein
URACIL-DNA GLYCOSYLASE / E.C.3.2.2.- / UDG / URACIL-DNA-GLYCOSYLASE


Mass: 25725.182 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P12295, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.96 Å3/Da / Density % sol: 68.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 20mM Tris-HCl, 100mM NaCl, 15% PEG 8000, pH 7.4, VAPOR DIFFUSION, HANGING DROP at 293K, temperature 293.0K
Crystal grow
*PLUS
Temperature: 293 K
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlprotein1drop
220 mMTris-HCl1droppH7.4
3100 mM1dropNaCl
415 %(w/v)PEG80001reservoir

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.35→20 Å / Num. all: 20394 / Num. obs: 20394 / % possible obs: 90.2 % / Observed criterion σ(I): 0 / Rsym value: 0.154 / Net I/σ(I): 6.9
Reflection shellResolution: 3.35→3.47 Å / Mean I/σ(I) obs: 1.4 / Rsym value: 0.369 / % possible all: 94.8
Reflection
*PLUS
Num. measured all: 38941 / Rmerge(I) obs: 0.154
Reflection shell
*PLUS
% possible obs: 94.8 % / Rmerge(I) obs: 0.369

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UUG

1uug


Resolution: 3.35→20 Å / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.326 1101 5.8 %RANDOM
Rwork0.241 ---
obs0.241 18979 84 %-
all-18979 --
Displacement parametersBiso mean: 28.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.4 Å
Luzzati d res low-10 Å
Luzzati sigma a0.51 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 3.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7157 0 0 175 7332
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_dihedral_angle_d27.1
X-RAY DIFFRACTIONx_improper_angle_d0.91
LS refinement shellResolution: 3.35→3.56 Å / Rfactor Rfree error: 0.027
RfactorNum. reflection% reflection
Rfree0.353 171 -
Rwork0.271 --
obs-2887 81.1 %
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.91

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more